Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis

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• 作者：Sajad Majeed Zargar ; Masayuki Fujiwara ; Shoko Inaba ; Mami Kobayashi…
• 关键词：Cosine correlation coefficients ; iTRAQ ; GLP5 ; PDR9/ABCG37 ; Quantitative proteomics
• 刊名：Plant Cell Reports
• 出版年：2015
• 出版时间：January 2015
• 年：2015
• 卷：34
• 期：1
• 页码：157-166
• 全文大小：733 KB
• 参考文献：1. Bacaicoa E, Mora V, Zamarreno AM, Fuentes M, Casanova E, Garcia-Mina JM (2011) Auxin: a major player in the shoot-to-root regulation of root Fe-stress physiological responses to Fe deficiency in cucumber plants. Plant Physiol Biochem 49:545-56 p://dx.doi.org/10.1016/j.plaphy.2011.02.018" target="_blank" title="It opens in new window">CrossRef
  2. Cailliatte R, Schikora A, Briat JF, Mari S, Curie C (2010) High-affinity manganese uptake by the metal transporter NRAMP1 is essential for Arabidopsis growth in low manganese conditions. Plant Cell 22:904-17 p://dx.doi.org/10.1105/tpc.109.073023" target="_blank" title="It opens in new window">CrossRef
  3. Cakmak I (2000) Possible roles of zinc in protecting plant cells from damage by reactive oxygen species. New Phytol 146:185-05 p://dx.doi.org/10.1046/j.1469-8137.2000.00630.x" target="_blank" title="It opens in new window">CrossRef
  4. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor M, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove LJ, Fernie AR (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142:1380-396 p://dx.doi.org/10.1104/pp.106.088534" target="_blank" title="It opens in new window">CrossRef
  5. Chen WW, Yang JL, Qin C, Jin CW, Mo JH, Ye T, Zheng SJ (2010) Nitric oxide acts downstream of auxin to trigger root ferric-chelate reductase activity in response to iron deficiency in Arabidopsis. Plant Physiol 154:810-19 p://dx.doi.org/10.1104/pp.110.161109" target="_blank" title="It opens in new window">CrossRef
  6. Colangelo EP, Guerinot ML (2004) The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response. Plant Cell 16:3400-412 p://dx.doi.org/10.1105/tpc.104.024315" target="_blank" title="It opens in new window">CrossRef
  7. Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320:942-45 p://dx.doi.org/10.1126/science.1153795" target="_blank" title="It opens in new window">CrossRef
  8. Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3:1128-134 p://dx.doi.org/10.1074/mcp.T400009-MCP200" target="_blank" title="It opens in new window">CrossRef
  9. Eckhardt U, Mas MA, Buckhout TJ (2001) Two iron-regulated cation transporters from tomato complement metal uptake-deficient yeast mutants. Plant Mol Biol 45:437-48 p://dx.doi.org/10.1023/A:1010620012803" target="_blank" title="It opens in new window">CrossRef
  10. Eide D, Broderius M, Fett J, Guerinot ML (1996) A novel iron-regulated metal transporter from plants identified by functional expression in yeast. Proc Natl Acad Sci USA 93:5624-628 p://dx.doi.org/10.1073/pnas.93.11.5624" target="_blank" title="It opens in new window">CrossRef
  11. El-Sharkawy I, Mila I, Bouzayen M, Jayasankar S (2010) Regulation of two germin-like protein genes during plum fruit development. J Exp Bot 61:1761-770 p://dx.doi.org/10.1093/jxb/erq043" target="_blank" title="It opens in new window">CrossRef
  12. Enfissi EMA, Barneche F, Ahmed I, Lichtle C, Gerrish C, McQuinn RP, Giovannoni JJ, Lopez-Juez E, Bowler C, Bramley PM, Fraser PD (2010) Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 down regulated tomato fruit. Plant Cell 22:1190-215 p://dx.doi.org/10.1105/tpc.110.073866" target="_blank" title="It opens in new window">CrossRef
  13. Fourcroy P, Sisó-Terraza P, Sudre D, Savirón M, Reyt G, Gaymard F, Abadía A, Abadia J, Alvarez-Fernández A, Briat JF (2014) Involvement of the ABCG37 transporter in secretion of scopoletin and derivatives by Arabidopsis roots in response to iron deficiency. New Phytol 201:155-67 p://dx.doi.org/10.1111/nph.12471" target="_blank" title="It opens in new window">CrossRef
  14. Fujiwara T, Hirai MY, Chino M, Komeda Y, Naito S (1992) Effects of sulfur nutrition on expression of the soybean seed storage protein genes in transgenic petunia. Plant Physiol 99:263-68 p://dx.doi.org/10.1104/pp.99.1.263" target="_blank" title="It opens in new window">CrossRef
  15. Fukao Y, Ferjani A, Tomioka R, Nagasaki N, Kurata R, Nishimori Y, Fujiwara M, Maeshima M (2011) iTRAQ analysis reveals mechanisms of growth defe
• 作者单位：Sajad Majeed Zargar (1) (2)
  Masayuki Fujiwara (1) (3)
  Shoko Inaba (1)
  Mami Kobayashi (1)
  Rie Kurata (3)
  Yoshiyuki Ogata (4)
  Yoichiro Fukao (1) (3)
  
  1. Plant Global Education Project Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, 8916-5, Ikoma, 630-0192, Japan
  2. School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, Jammu and Kashmir, 180009, India
  3. Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
  4. Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Plant Sciences
  Biotechnology
  Plant Biochemistry
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-203X

文摘

Key message For discovering the functional correlation between the identified and quantified proteins by iTRAQ analysis, here we propose a correlation analysis method with cosine correlation coefficients as a powerful tool. Abstract iTRAQ analysis is a quantitative proteomics approach that enables identification and quantification of a large number of proteins. In order to obtain proteins responsive to Zn, Mn, or Fe mineral deficiency, we conducted iTRAQ analysis using a microsomal fraction of protein extractions from Arabidopsis root tissues. We identified and quantified 730 common proteins in three biological replicates with less than 1?% false discovery rate. To determine the role of these proteins in tolerating mineral deficiencies and their relation to each other, we calculated cosine correlation coefficients and represented the outcomes on a correlation map for visual understanding of functional relations among the identified proteins. Functionally similar proteins were gathered into the same clusters. Interestingly, a cluster of proteins (FRO2, IRT1, AHA2, PDR9/ABCG37, and GLP5) highly responsive to Fe deficiency was identified, which included both known and unknown novel proteins involved in tolerating Fe deficiency. We propose that the correlation analysis with the cosine correlation coefficients is a powerful method for finding important proteins of interest to several biological processes through comprehensive data sets.